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Case Studies3

Case Studies

Plants

 OrganismProduct usedJournalYearAuthorTitleLink to Publication
Plants       
 BarleyLTCPlant Physiology2014Ariyadasa et al.A Sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphismsLink
 EucalyptusMultipointNew Phytologist2009Foucart et al.Overexpression of EgROP1, a Eucalyptus vascular‐expressed Rac‐like small GTPase, affects secondary xylem formation in Arabidopsis thaLink
 MaizeMultipointGenetics2006Fu et al.Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of MaizeLink
 Maritime PineMultiQTLPlant, Cell and Environment2002Brendel et al.Genetic parameters and QTL analysis of δ13C and ring width in maritime pineLink
 Maritime PineMultipoint, MultiQTLJournal of Experimental Botany2014Marguerit et al.The genetics of water-use efficiency and its relation to growth in maritime pineLink
 OatMultipoint – ConsensusThe Plant Genome2016Chaffin et al.A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome RearrangementLink
 PoplarMultiQTLNew Phytologist2010Rohde et al.Bud set in poplar – genetic dissection of a complex trait in natural and hybrid populationsLink
 PopulusMultiQTLThe Plant Journal2006Morreel et al.Genetical metabolomics of flavonoid biosynthesis in Populus: a case studyLink
 PopulusMultiQTLFood and Energy Security2013Viger et al.Toward improved drought tolerance in bioenergy crops: QTL for carbon isotope composition and stomatal conductance in PopulusLink
 Potato BeanMultipointTheoretical and Applied Genetics2018Singh et al.A transcriptome‑SNP‑derived linkage map of Apios Americana (potato bean) provides insights about genome re‑organization and synteny conservation in the phaseoloid legumesLink
 RapeseedMultipointDNA Research2012Raman et al.Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.).Link
 RiceMultiQTLNature/Scientific Reports2017Liu et al.Characterization of a major QTL for manganese accumulation in rice grainLink
 RyegrassLTCAnnals of Botany2019Harper et al.Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traitsLink
 Silene LatifoliaMultiQTLEvolution2006Scotti & Delph.Selective trade-offs and sex-chromosome evolution in Silene latifoliaLink
 SorghumMultipointBMC Genomics2008Mace et al.DArT markers: diversity analyses and mapping in Sorghum bicolorLink
 SugarcaneMultipoint, MultiQTLEuphytica2013Singh et al.Genetic mapping and QTL analysis for sugar yield-related traits in sugarcaneLink
 Sweet CherryMultiQTLNature/Scientific Reports2019Cai et al.A fruit firmness QTL identified on linkage group 4 in sweet cherry (Prunus avium L.) is associated with domesticated and bred germplasmLink
 WatermelonMultiPoint – UltradenseG32014Reddy et al.High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelonLink
 WheatLTCInternational Plant and Animal Genome Conference XX2012Frenkel et al.Contig Anchoring of Wheat Chromosome1BS Using LTC Analytical ToolsLink
 WheatLTCGenome Biology2013Raats et al.The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolutionLink
 WheatMultipointThe Plant Journal2016Phan et al.Differential effector gene expression underpins epistasis in a plant fungal diseaseLink
 WheatLTCGenome Biology2018Keeble-Gagnèr et al.Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genomeLink
 WheatMultipointNature/Nature Communications2018Klymiuk et al.Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase familyLink
 WheatMultipoint, MultiQTLScience2018Appels et al.Shifting the limits in wheat research and breeding using a fully annotated reference genomeLink
 WheatMultipointPNAS2019Sakuma et al.Unleashing floret fertility in wheat through the mutation of a homeobox geneLink
 White SpruceMultiQTLBMC Genomics2011Pelgas et al.QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environmentsLink
 Wild Emmer WheatMultiQTLPNAS2003Peng et al.Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheatLink
 Wild Emmer WheatMultiQTLBioRXIV2019Fatiukha et/ al.Grain Protein Content QTLs Identified in a Durum × Wild Emmer Wheat Mapping Population Tested in Five EnvironmentsLink

Plants

 OrganismProduct usedJournalYearAuthorTitleLink to Publication
Plants       
 BarleyLTCPlant Physiology2014Ariyadasa et al.A Sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphismsLink
 EucalyptusMultipointNew Phytologist2009Foucart et al.Overexpression of EgROP1, a Eucalyptus vascular‐expressed Rac‐like small GTPase, affects secondary xylem formation in Arabidopsis thaLink
 MaizeMultipointGenetics2006Fu et al.Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of MaizeLink
 Maritime PineMultiQTLPlant, Cell and Environment2002Brendel et al.Genetic parameters and QTL analysis of δ13C and ring width in maritime pineLink
 Maritime PineMultipoint, MultiQTLJournal of Experimental Botany2014Marguerit et al.The genetics of water-use efficiency and its relation to growth in maritime pineLink
 OatMultipoint – ConsensusThe Plant Genome2016Chaffin et al.A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome RearrangementLink
 PoplarMultiQTLNew Phytologist2010Rohde et al.Bud set in poplar – genetic dissection of a complex trait in natural and hybrid populationsLink
 PopulusMultiQTLThe Plant Journal2006Morreel et al.Genetical metabolomics of flavonoid biosynthesis in Populus: a case studyLink
 PopulusMultiQTLFood and Energy Security2013Viger et al.Toward improved drought tolerance in bioenergy crops: QTL for carbon isotope composition and stomatal conductance in PopulusLink
 Potato BeanMultipointTheoretical and Applied Genetics2018Singh et al.A transcriptome‑SNP‑derived linkage map of Apios Americana (potato bean) provides insights about genome re‑organization and synteny conservation in the phaseoloid legumesLink
 RapeseedMultipointDNA Research2012Raman et al.Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.).Link
 RiceMultiQTLNature/Scientific Reports2017Liu et al.Characterization of a major QTL for manganese accumulation in rice grainLink
 RyegrassLTCAnnals of Botany2019Harper et al.Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traitsLink
 Silene LatifoliaMultiQTLEvolution2006Scotti & Delph.Selective trade-offs and sex-chromosome evolution in Silene latifoliaLink
 SorghumMultipointBMC Genomics2008Mace et al.DArT markers: diversity analyses and mapping in Sorghum bicolorLink
 SugarcaneMultipoint, MultiQTLEuphytica2013Singh et al.Genetic mapping and QTL analysis for sugar yield-related traits in sugarcaneLink
 Sweet CherryMultiQTLNature/Scientific Reports2019Cai et al.A fruit firmness QTL identified on linkage group 4 in sweet cherry (Prunus avium L.) is associated with domesticated and bred germplasmLink
 WatermelonMultiPoint – UltradenseG32014Reddy et al.High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelonLink
 WheatLTCInternational Plant and Animal Genome Conference XX2012Frenkel et al.Contig Anchoring of Wheat Chromosome1BS Using LTC Analytical ToolsLink
 WheatLTCGenome Biology2013Raats et al.The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolutionLink
 WheatMultipointThe Plant Journal2016Phan et al.Differential effector gene expression underpins epistasis in a plant fungal diseaseLink
 WheatLTCGenome Biology2018Keeble-Gagnèr et al.Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genomeLink
 WheatMultipointNature/Nature Communications2018Klymiuk et al.Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase familyLink
 WheatMultipoint, MultiQTLScience2018Appels et al.Shifting the limits in wheat research and breeding using a fully annotated reference genomeLink
 WheatMultipointPNAS2019Sakuma et al.Unleashing floret fertility in wheat through the mutation of a homeobox geneLink
 White SpruceMultiQTLBMC Genomics2011Pelgas et al.QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environmentsLink
 Wild Emmer WheatMultiQTLPNAS2003Peng et al.Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheatLink
 Wild Emmer WheatMultiQTLBioRXIV2019Fatiukha et/ al.Grain Protein Content QTLs Identified in a Durum × Wild Emmer Wheat Mapping Population Tested in Five EnvironmentsLink

Animals

OrganismProduct usedJournalYearAuthorTitleLink to Publication
Fish
Arctic CharrMultiQTLEvolution and Development2014Küttner et al.Hidden genetic variation evolves with ecological specialization: the genetic basis of phenotypic plasticity in Arctic charr ectomorphsLink
Atlantic SalomonMultiQTLNature2004Reid et al.QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus)Link
Cave fishMultiQTLEvolution and Development2008Protas et alMulti-trait evolution in a cave fish, Astyanax mexicanusLink
Cave fishMultiQTLMolecular Biology and Evolution2013Bradic et al.The Population Genomics of Repeated Evolution in the Blind Cavefish Astyanax mexicanusLink
Grey mulletMultipointAnimal Genetics2016Dor et al.Identification of the sex-determining region in flathead grey mullet (Mugil cephalus)Link
TroutMultiQTLBMC Genetics2010Wringe et alGrowth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss)Link
Animals
CattleMultiQTLPNAS2003Hanotte et al.Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N’Dama and susceptible East African Boran cattleLink
ChickenMultiQTLCytogenetic and Genome Research2007Atzmon et al.Detection of agriculturally important QTLs in chickens and analysis of the factors affecting genotyping strategyLink
MiceMultiQTLGenome Research2001Valenza-Schaerly et al.A Dominant Modifier of Transgene Methylation Is Mapped by QTL Analysis to Mouse Chromosome 13Link
MiceMultipointJournal of Neuroscience2003Steinberger et al.Genetic Mapping of Variation in Spatial Learning in the MouseLink
MiceMultiPoint – UltradenseMammalian Genome2006Behnke et al.High resolution mapping of chromosomal regions controlling resistance to gastrointestinal nematode infections in an advanced intercross line of miceLink
MiceMultiQTLInternational Immunology2009Jiang et al.Identification of QTLs that modify peripheral neuropathy in NOD.H2b–Pdcd12/2 miceLink
RatMultiQTLGenome Research2002Fernández-Teruel et al.A Quantitative Trait Locus Influencing Anxiety in the Laboratory RatLink
RatMultiQTLObesity2014Marissal-Arvy et al.QTLs Influencing Carbohydrate and Fat Choice in a LOU/CxFischer 344 F2 Rat Population.Link
SalamandersMultiQTLGenome Biology and Evolution2013Page et al.Genomics of a Metamorphic Timing QTL: met1 Maps to a Unique Genomic Position and Regulates Morph and Species-Specific Patterns of Brain TranscriptionLink
WaspsMultipointNature/Heredity2010Beukeboom et alA comparison of recombination frequencies in intraspecific versus interspecific mapping populations of NasoniaLink
WaspsMultiPoint – UltradenseG32013Desjardins et al.Fine-Scale Mapping of the Nasonia Genome to Chromosomes Using a High-Density Genotyping MicroarrayLink

Multi-organism

 OrganismProduct usedJournalYearAuthorTitleLink to Publication
        
 Salamanders, chicken, humanMultipointGenome Research2010Voss et al.Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomesLInk
  MultipointNature Communications2012Tapia et al.Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteinsLInk
        

Multi-organism

 OrganismProduct usedJournalYearAuthorTitleLink to Publication
        
 Salamanders, chicken, humanMultipointGenome Research2010Voss et al.Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomesLInk
  MultipointNature Communications2012Tapia et al.Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteinsLInk